rs6894312

Positions:

• chr5-18676174-T-C
• chr5-18676174-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.861 in 151,882 control chromosomes in the GnomAD database, including 56,761 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.86 (56761 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.651

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.951 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.861 AC: 130696 AN: 151764 Hom.: 56694 Cov.: 31

Gnomad AFR AF: 0.959

Gnomad AMI AF: 0.663

Gnomad AMR AF: 0.861

Gnomad ASJ AF: 0.790

Gnomad EAS AF: 0.916

Gnomad SAS AF: 0.858

Gnomad FIN AF: 0.819

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.811

Gnomad OTH AF: 0.859

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.861 AC: 130823 AN: 151882 Hom.: 56761 Cov.: 31 AF XY: 0.861 AC XY: 63908 AN XY: 74216

Gnomad4 AFR AF: 0.959

Gnomad4 AMR AF: 0.861

Gnomad4 ASJ AF: 0.790

Gnomad4 EAS AF: 0.916

Gnomad4 SAS AF: 0.858

Gnomad4 FIN AF: 0.819

Gnomad4 NFE AF: 0.811

Gnomad4 OTH AF: 0.861

Alfa AF: 0.824 Hom.: 4310

Bravo AF: 0.867

Asia WGS AF: 0.903 AC: 3130 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.54
DANN	Benign	0.62

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs6894312; hg19: chr5-18676283;